Search Results for "compiler python linux" - Page 8
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Showing 364 open source projects for "compiler python linux"
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hrefinder
Detection of homologous recombination events from SNP data
This software detects homologous recombination events (HREs) from SNP data. Based on SNP alleles calls and locations, it breaks the genomes into locally colinear blocks, and looks for cases where SNPs do not agree with the vertical pattern of inheritance in a phylogeny. It applies a dynamic programming algorithm to model whether changes within a block are likely a result of mutations, sequencing errors, or HRE. We use information from the nearby SNPs, so that if 1-2 alleles in a series of... -
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ReferenceFree
Scripts for reference free genomic analysis
These are Python scripts plus C/C++ programs for automating the reference free genomic analysis described in: Kua C-S, Ruan J, Harting J, Ye C-X, Helmus MR, et al. (2012) Reference-Free Comparative Genomics of 174 Chloroplasts. PLoS One 7(11). http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0048995 Analytical concept conceived by CHCannon and CSKua. Original script written in Mathematica by CHCannon. -
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ARDEN
Specificity Control for Read Alignments Using an Artificial Reference
We introduce ARDEN (Artificial Reference Driven Estimation of false positives in NGS data), a novel benchmark that estimates error rates based on real experimental reads and an additionally generated artificial reference genome. It allows the computation of error rates specifically for a dataset and the construction of a ROC-curve. Thereby, it can be used to optimize parameters for read mappers, to select read mappers for a specific problem or also to filter alignments based on quality estimation. -
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AMBIENT
Find active modules in metabolic networks using high-throughput data
IMPORTANT: Since publication of the AMBIENT method in BMC Sys Bio, several updates have been made. If you wish to use the version used in the paper it is v0.6.3, however I recommend using the latest version which works in the same way but with additional options and has stability and performance improvements. Thanks for your interest! AMBIENT (Active Modules for Bipartite Networks) is a Python module that uses simulated annealing to find areas of a metabolic network (modules) that have... -
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A set of very optimized tools for indexing/querying huge genomes/files. Provided so far: a very fast exact mapper, and an unconstrained split-mapper
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GS junior Webserver
GS junior Webserver
GS junior Webserver is a web based file server to easily access sequencing data of -
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The igraph library
Library for creating and manipulating graphs
This is a library for creating and manipulating graphs with focus on speedy operations for large, sparse graphs. -
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Application to create 'electronic fluorescent pictographic' representations of gene expression patterns. Created at the Provart lab of the department of Cell & Systems Biology, University of Toronto.
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GEPETTO - Gene Prioritization in Java
GEPETTO (GEne Prioritization ExTended TOol)
GEPETTO (GEne PrioriTization ExTended TOol) is an original open-source framework, distributed under the LGPL license, for gene selection and prioritization on a desktop computer that ensures confidentiality of personal data. It takes advantage of the data integration capabilities in the SM2PH-Central Framework(KD4v,MSV3d,BIRD,..), combined with in-house developed gene prioritization methods. It currently incorporates six prioritization modules, based on gene sequence, protein-protein... -
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StabiTissue
3D Stabilization software for intravital imaging of mouse organs
- 2D Stabilization in each slice of the stacks in time. - 3D Stabilization intravital imaging of all the stacks (including the dimension Z) - create the videos and the stabilized images in a new folder -
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SpiKeDeteKt
An automatic spike detection program to be used with new KlustaKwik
This is an automatic spike detection program which takes account of probe geometry and produces a .mask file to be used with the new masked version of KlustaKwik. We recommend you use Python 2.6 or 2.7, e.g. a free academic version can be obtained from Entthought Python. The input files for SpiKeDeteKt are: .dat (raw data file) .probe (probe file, described below - user constructed) parameters.py (optional - otherwise it uses defaultparameters.py) SpiKeDeteKt outputs... -
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Laboratory notebook using version control system and independent date-time stamping (as notarization), in order to ensure record accountability, auditing, and conforming to US FDA 21 CFR 21's rule on electronic records. Please kindly rate this application or drop me an email at [ mauriceling AT acm DOT org ] so that I can hear from you. Otherwise, I have no idea who the users are. Please kindly help.
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The PyCogent project is moving to GitHub. When completed, you will find us at http://github.com/pycogent/pycogent/. You can find the PyCogent website at http://www.pycogent.org.
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CoNIFER
Homepage for CoNIFER (Copy Number Inference From Exome Reads)
CoNIFER uses exome sequencing data to find copy number variants (CNVs) and genotype the copy-number of duplicated genes. -
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Prediction of MHC class I- and MHC class II-restricted T-cell epitopes. Prediction of proteasomal/immunoproteasomal processing of antigens. Prediction of peptide-TAP binding.
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Pysimony
A Pythonic Implementation of Parsimony Inference of Phylogeny
UPDATE: After some bug fixes, I've ditched Pysimony for Javamony: https://sourceforge.net/projects/javamony/ Given Python's beauty, I know that someday I will have to finish Pysimony. A student's first attempt at a phylogenetic inference program, written in the simplistic yet elegant Python. Pysimony reads a FASTA file (only ATGC accepted) specified as its only argument. Basic testing has shown that it is slow, inaccurate and most definitely inefficient. An... -
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u/sbmv2012
Taxonomy assignment of metazoans using a python based pipeline
The aim of this project is to create an automated pipeline for taxonomic assignment of DNA sequences obtained from environmental samples. We develop a series of python scripts to process the raw sequence data obtained from benthic environmental samples and to taxonomical assignment of these sequences and finally to integrate all data in a relational database. -
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pyBioImage
Biological Imaging Software suite
The pyBioImage is a python a python based biological imaging suite tailored to the problem of finding Germinal Center "spots" within multidimensional microscopy images as it is described in the research paper: "Software tool for 3D extraction of germinal centers", by David N. Olivieri, Merly Escalona and Jose Faro. -
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Primer Design Tool
Design PCR primers
A simple tool to design DNA primers for mutagenesis in BGME lab (JHU). Allows users to select or enter background sequence and add current and new mutations. During the design process, users are presented with various updating checks to guide them. -
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brocc
BLAST Read and OTU Consensus Classifier
NOW HOSTED ON GITHUB: https://github.com/kylebittinger/brocc Old releases are kept here for archival purposes. -
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GemSIM is a software package for generating realistic simulated next-generation sequencing reads with quality score values. Both Illumina and Roche/454 reads (single or paired end) can be simulated using appropriate empirical error models.
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QUASR
Cross-platform NGS processing and analysis pipeline in Python
QUASR is a lightweight pipeline written to process and analyse next-generation sequencing (NGS) data from Illumina, 454, and Ion Torrent platforms. Although originally written for viral data, it is generic enough to work on any NGS dataset. Functions include: duplicate removal demultiplexing primer-removal quality-assurance (QA) graphing quality control (QC) consensus-generation minority-variant determination minority-variant graphing The main current version is 6.X, which is... -
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The QIIME project has moved to GitHub. You can now find us at http://github.com/qiime/. As always, you can find the QIIME website at http://www.qiime.org.
